When referencing this page, please use this url: http://blanco.biomol.uci.edu/mpstruc/
 

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  • Membrane-embedded structures now available!: Mark Sansom's lab at Oxford has created the MemProtMD database of all known transmembrane proteins embedded in lipid membranes, described in Stansfeld et al. (2015) Structure 23:1350-1361. Links to the structures are now included in mpstruc. Click on the icon, and you will be taken to the appropriate entry in MemProtMD.
  • MPtopo XML data representations now available: XML representations are now available for the MPtopo membrane protein topology database.
  • MPtopo integrated into mpstruc: MPtopo, our curated database of membrane proteins with experimentally validated transmembrane segments, has a new structure and interface: It is now integrated with mpstruc (e.g., see the mpstruc entry for 2BRD for a link to mptopo). MPEx has also been updated to use the new mptopo.

Latest new protein entered: 05 Oct 2018 at 16:53 PDT.
Last database update: 05 Oct 2018 at 16:53 PDT

New Structures:
Unique proteins in database = 831
Coördinate files in database = 2638
Published reports of membrane protein structures in database = 1480
(Counts do not include pre-publication structures)
A full list of pdb codes currently in the database is available here.

Unique proteins include proteins of same type from different species. For example, photosynthetic reaction centers from R. viridis and R. sphaeroides are considered unique. Structures of mutagenized versions of proteins already in the database are excluded as unique. Proteins that differ only by substrate bound or by physiological state are also excluded. Structures 'obsoleted' by the PDB are not included.

Total number of PDB coördinate files, including those for unique proteins. This number reflects the fact that published reports of structures often include several coördinate files describing, for example, the protein in different crystal forms, or with different bound substrates.


Pre-Publication Structures (link to mpstruc bulletin board page)
 
A word about the new interface to the protein table.

There are other ways of viewing the data in the mpstruc database besides the hierarchical view presented in the table on this page. The mpstruc database queries page (follow the above link) provides a list of queries on the database, some of which provide tables with sortable columns. Some of the queries may take a few moments. Query results are also available as XML data.

Currently available queries include requesting a list of unique proteins, a list of all published reports, counting unique proteins by year, and counting all published reports by year.

XML Representations

An XML representation provides a convenient machine or human readable format of the portion of the data table that has been made visible, and allows you to build software tools to consume it as you see fit. You can use the URLs adjacent to the buttons below to access the same view the corresponding button provides.

This button generates an XML representation of the currently visible portion of the table.

//blanco.biomol.uci.edu/mpstruc/listAll/mpstrucTblXml
//blanco.biomol.uci.edu/mpstruc/listAll/mpstrucMonotopicTblXml
//blanco.biomol.uci.edu/mpstruc/listAll/mpstrucBetaBrlTblXml
//blanco.biomol.uci.edu/mpstruc/listAll/mpstrucAlphaHlxTblXml

If your browser doesn’t directly display a nicely formatted XML page, it should provide a "view page source" menu selection that will. It should also provide a "save page" option so that you can download the XML formatted data.

If you’re not familiar with XML and how to use it, a good source of information is available here.

NOTES:

Generated XML uses the following Document Type Definition (DTD):

<!DOCTYPE mpstruc [
  <!ELEMENT mpstruc (caption,groups*)>
  <!ATTLIST mpstruc createdBy CDATA #REQUIRED>
  <!ATTLIST mpstruc maintainedBy CDATA #REQUIRED>
  <!ATTLIST mpstruc copyright CDATA #REQUIRED>
  <!ATTLIST mpstruc url CDATA #REQUIRED>
  <!ATTLIST mpstruc lastNewProteinDate CDATA #REQUIRED>
  <!ATTLIST mpstruc lastDatabaseEditDate CDATA #REQUIRED>
  <!ATTLIST mpstruc timeStamp CDATA #REQUIRED>
  <!ELEMENT caption (#PCDATA)>
  <!ELEMENT groups (group*)>
  <!ELEMENT group (name,proteins,subgroups)>
  <!ELEMENT subgroups (subgroup*)>
  <!ELEMENT subgroup (name,proteins)>
  <!ELEMENT name (#PCDATA)>
  <!ELEMENT proteins (protein*)>
  <!ELEMENT memberProteins (memberProtein*)>
  <!ELEMENT protein (pdbCode,name,species,taxonomicDomain,expressedInSpecies,resolution,description,bibliography,
                     secondaryBibliographies,relatedPdbEntries,memberProteins)>
  <!ELEMENT memberProtein (pdbCode,masterProteinPdbCode,name,species,expressedInSpecies,resolution,
                           description,bibliography,secondaryBibliographies,relatedPdbEntries)>
  <!ELEMENT pdbCode (#PCDATA)>
  <!ELEMENT masterProteinPdbCode (#PCDATA)>
  <!ELEMENT species (#PCDATA)>
  <!ELEMENT taxonomicDomain (#PCDATA)>
  <!ELEMENT expressedInSpecies (#PCDATA)>
  <!ELEMENT resolution (#PCDATA)>
  <!ELEMENT description (#PCDATA)>
  <!ELEMENT bibliography (pubMedId,authors,year,title,journal,volume,issue,pages,doi,notes)>
  <!ELEMENT pubMedId (#PCDATA)>
  <!ELEMENT authors (#PCDATA)>
  <!ELEMENT year (#PCDATA)>
  <!ELEMENT title (#PCDATA)>
  <!ELEMENT journal (#PCDATA)>
  <!ELEMENT volume (#PCDATA)>
  <!ELEMENT issue (#PCDATA)>
  <!ELEMENT pages (#PCDATA)>
  <!ELEMENT doi (#PCDATA)>
  <!ELEMENT notes (#PCDATA)>
  <!ELEMENT secondaryBibliographies (bibliography*)>
  <!ELEMENT relatedPdbEntries (pdbCode*)>
]>

 
Links to the Protein Data Bank Site
Links to the Structural Biology Knowledgebase Site
Membrane Proteins of Known 3D Structure
(Table description)
Protein
PDB Code Links Reference
(links are to PubMed)
MONOTOPIC MEMBRANE PROTEINS
TRANSMEMBRANE PROTEINS: BETA-BARREL
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Adventitious Membrane Proteins: Alpha-helical Pore-forming Toxins.
De novo Designed Membrane Proteins
Functional Proteins Designed from First Principles
Outer Membrane Proteins
Bacterial Cell Divison Proteins
These proteins comprise the so-called 'divisome'
Bacterial and Algal Rhodopsins
Novel Receptors
Tetraspanins
Mediate essential functions in the immune, reproductive, genitourinary, and auditory systems
Autonomously Folding "Membrane Proteins" (Sec-independent)
Virus Coat Proteins
Glycoproteins
High-Density Lipoprotein (HDL) Receptors
Tumor Necrosis Factor (TNF) Receptor Superfamily
Receptor Tyrosine Kinase (RTK) Family
Single-span TM proteins important in cellular signalling
Epidermal Growth Factor Receptors (EGFRs)
ErbB (or HER) family of receptor tyrosine kinases (RTKs)
Erythropoietin-Producing Hepatocellular Receptors
Eph family of receptor tyrosine kinases (RTKs)
Fibroblast Growth Factor Receptors
FGFR family of receptor tyrosine kinases (RTKs)
Vascular Endothelial Growth Factor Receptors
VEGFR family of receptor tyrosine kinases (RTKs)
Integrin Adhesion Receptors
Adiponectin Receptors
7TM receptors with inverted topology relative to GPCR receptors
Adiponectin is a protein hormone that is important in glucose & fatty acid metabolism
G Protein-Coupled Receptors (GPCRs)
Wikipedia Entry
GPCRdb Home Page
GPCR Network Home Page
Histidine Kinase Receptors
Immune Receptors
SNARE Protein Family
Claudins
Claudins form the backbone of tight junctions
TMEM16 Family Proteins
A functionally diverse family of proteins also known as Anoctamins
Channels: Mechanosensitive
Channels: Potassium, Sodium, & Proton Ion-Selective
Channels: Calcium Ion-Selective
Channels: Transient Receptor Potential (TRP)
Non-selective cation channels responding to a wide range of chemical and physical stimuli
Channels: Other Ion Channels
Channels: Fluc Family
These are F--selective channels
Channels: Aquaporins and Glyceroporins
Channels : Formate/Nitrite Transporter (FNT) Family
Channels: Urea Transporters
Channels: Gap Junctions
Channels: Intercellular
Channels found in sporulating bacteria that connect mother cell to forespore
Channels: Amt/Mep/Rh proteins
Cys-Loop Receptor Family
Cation-selective and Anion-selective Ligand-gated Channels
Cation-selective include nicotinic acetylcholine and serotonin 5-HT3 receptors. Anion-selective include γ-aminobutyric, glycine, and invertebrate glutamate-gated chloride channels (GluCl)
Sec and Translocase Proteins
Membrane Proteins Involved with Protein Secretion and Insertion
formerly listed as "Channels: Protein-Conducting"
Celluose Synthases
Membrane Imbedded Glycosyltransferases
These use UDP-activated glucose to elongate nascent polysaccharides processively across membranes.
PNPT Superfamily
PNPT: polyprenylphosphate N-acetyl hexosamine 1-phosphate transferase
Proteins in this superfamily are responsible for the synthesis of cell envelope polymers
Shape, Elongation, Division, and Sporulation (SEDS) Proteins
Oligosaccharyltransferases (OST)
Catalyses Asparagine-linked (N-linked) Glycosylation
Glycosyltransfereases
Diacylglyceryl Transferases
Liponucleotide Synthetases
Cytidine-Diphosphate Diacylglycerol Synthetase is the prominent member of the family
N-acyltransferases
S-acyltransferases
Eukaryotic proteins that catalyze protein palmitoylation
Phosphoethanolamine (PEA) Transferases
Methyltransferases
Phosphotransferases
Phosphatidic Acid Phosphatases
Membrane-integrated type II phosphatidic acid phosphatases (PAP2)
UbiA Prenyltransferases
These enzymes are involved in the biosynthesis of a wide range molecules, including respiratory lipoquinones and archael lipids
Phosphoenolpyruvate-Dependent Phosphotransferases (PTSs)
Membrane-Bound Metalloproteases
CorA Superfamily Ion Transporters
Channels and transporters for divalent cation homeostasis. These have a membrane domain in series with a cytoplasmic domain that together form a continuous channel.
Bacterial Mercury Detoxification Proteins
Rhodaneses
Thiosulfate-Cyanide sulfurtransfereases
Drug/Metabolite Transporter (DMT) Superfamily
Multi-Drug Efflux Transporters
Members of the multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) transporter superfamily
AbgT Family of Transporters
Involved in bacterial folate synthesis through catabolite transport
Proteins in this family may also function as drug efflux pumps
Sulfate-Uptake Transporters/Permeases
Membrane-Associated Proteins in Eicosanoid and Glutathione Metabolism (MAPEG)
SWEET and semiSWEET Transporters, and Their Relatives
SWEETs are monsaccharide and disaccharide transporters. Bacterial homologues are semiSWEETS.
Major Facilitator Superfamily (MFS) Transporters
Solute Sodium Symporter (SSS) Family
Solute Carrier (SLC) Transporter Superfamily
Active transporters that use Na+ or H+ electrochemical gradients
Translocator Protein (18 kDA) TSPO
Principally an outer mitochondrial membrane protein that binds to cholesterol and drug ligands, but occurs in diverse organisms
Previously referred to as a peripheral-type benzodiazepine receptor (PBR). In mitochondria, it is part of large multimeric complex located in the outer mitochondrial membrane, and is closely associated with VDAC.
Ca2+:Cation Antiporter (CaCA) Family
Nucleobase-Cation-Symport-1 (NCS1) Family
Nucleobase-Cation-Symport-2 (NCS2) Family
also known as nucleobase/ascorbate transporter (NAT)
Solute Carrier Family 4 (anion exchanger)
Betaine/Choline/Carnitine Transporter (BCCT) Family
Amino Acid/Polyamine/Organocation (APC) Superfamily
Amino Acid Secondary Transporters
Cation Diffusion Facilitator (CDF) Family
Antiporters
Apical Sodium-Dependent Bile Acid Transporters (ASBT)
Energy-Coupling Factor (ECF) Transporters
ATP Binding Cassette (ABC) Transporters
CDP-Alcohol Phosphotransferases
These enzymes facilitate the conjugation of polar headgroups to diacylglycerol lipid tails
Insulin-Induced Gene Products: Insig Proteins
These are components of the sterol regulatory element-binding protein (SREBP) pathway
Sterol Reductases
Sterol-Sensing Domain (SSD) Proteins
These proteins are involved in cholesterol trafficking in the cholesterol-uptake pathway
Fatty Acid Desaturases
These enzymes maintain the cellular balance of saturated and monounsaturated lipids
Superfamily of K+ Transporters (SKT proteins)
Membrane-Integral Pyrophosphatases (M-PPases)
Ion-Translocating Pyrophosphatases Link Pyrophosphate (PPi) Hydrolysis to Sodium or Proton Pumping
V-ATPases and H+-PPases coexist on plant vacuolar membranes
Bacterial V-type ATPase
Also called A-type ATPase
Vacuolar ATPase (V-ATPase)
Eukaryotic V-ATPases
F-type ATPase
P-type ATPase
Hydrolases
Oxygenases
Transhydrogenases
Mo/Wbis-MGD Oxidoreductases
Oxidoreductases
Electron Transport Chain Complexes: Complex I
Electron Transport Chain Complexes: Complex II
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Information about Cytochrome bc1
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
( Information about cytochrome c oxidases)
Electron Transport Chain Super Complexes (Respirasome)
Nitric Oxide Reductases
Photosystems
Photosystem+Light-Harvesting Complex Supercomplex
Photoprotection Proteins
These proteins limit photo-oxidative damage to plants
Light-Harvesting Complexes
Photosynthetic Reaction Centers
Light-Harvesting+Reaction Center Complexes
H+/Cl- or F- Exchange Transporters

Description of Table

The table above is initially presented in a collapsed form, and the user can expand different sections of the table, or the entire table, and bookmark different sections of the table, or a fully expanded table version of the page, using the , , , and icons on the left margin of the table section headers.

mpstruc Taxonomic Domain data are derived from the UniProt Knowledgebase, which is based on the NCBI taxonomy database. These taxa can be searched for using 'Text Search of Table', above. The following icons are used in the table, as appropriate:

The table provides useful information about integral membrane proteins whose crystallographic, or sometimes NMR or cryo-EM, structures have been determined to a resolution sufficient to identify TM helices of helix-bundle membrane proteins (typically 4 - 4.5 Å). Reference is made to all of the protein types whose structures have been determined. We have attempted to make the database as inclusive as possible. If you find errors or omissions, please send a message to Stephen White.

 

The figure at the top right of the page shows the progress of membrane protein structure determination. The figure may be used freely in seminar presentations provided that the URL and lab information on the image are not removed. We thank Ahmed Bakan for bringing some counting errors to our attention, and Tony Crofts, Kenneth Rudd, and Ilan Samish for bringing missing structures to our attention. If structures are missing, please let us know. Send comments and suggestions to Stephen White or Craig Snider.

This database emphasizes structures determined by diffraction methods, although some NMR structures are included. A comprehensive list of NMR-determined structures is available from Dror Warschawski.

 

mpstruc has a new user interface to help accommodate the growing size of the protein data table. The dynamic nature of this new interface is handled by your browser, and so, your particular browser, its configuration, and your hardware configuration all may have an impact on the interface performance.

We've found that, in general, contemporary versions of Firefox, Chrome, and Safari provide the best performance. Internet Explorer performs well, but is a bit awkward when attempting to create a bookmark for this page to open with an expanded table (preparing the proper URL requires a page reload). This may also be an issue for older versions of the previously mentioned browsers.

The Opera browser, while full featured, seems to be the slowest browser of those we've tested. If this is your favorite browser, you may want to bookmark an expanded table version of the page, and avoid using the dynamic features of the table.

Of course, browser providers are providing frequent updates of their products, so these observations may be out of date by the time you read this.

By the way, you can use the icons to bookmark sections of the table. That icon in the table header allows you to create a bookmark for this page with the table fully expanded.

If you discover any issues with this interface, please let us know. We want to make this resource as useful as possible!